Nextflow Registry | nf-core/wisecondorx/predict@0.0.0-6c4ed3a

nf-core/wisecondorx/predict @ 0.0.0-6c4ed3a

Find copy number aberrations

copy number variation bed npz png

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

Find copy number aberrations

Add the following snippet to your workflow script to include this module.

include { WISECONDORX_PREDICT } from 'nf-core/wisecondorx/predict'

MIT License

Process

`Name`	`WISECONDORX_PREDICT`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`npz` file	An NPZ file created with WisecondorX convert `*.npz`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test', single_end:false ]
`reference` file	A reference NPZ file created with WisecondorX newref `*.npz`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`blacklist` file	OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small) `*.bed`

Output 7 channels

#1 bins_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`*_bins.bed` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_bins.bed`

#2 chr_plots tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`[!genome_wide]*.png` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `[!genome_wide]*.png`

#3 genome_plot tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`genome_wide.png` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `genome_wide.png`

#4 segments_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`*_segments.bed` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_segments.bed`

#5 chr_statistics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`*_statistics.txt` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_chr_statistics.txt`

#6 aberrations_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`
`*_aberrations.bed` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*_aberrations.bed`

#7 versions_wisecondorx tuple

`${task.process}` string	The name of the process
`wisecondorx` string	The name of the tool
`pip list \|& sed -n 's/wisecondorx *//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
wisecondorx	WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes	https://github.com/CenterForMedicalGeneticsGhent/WisecondorX